AMBER Archive (2005)

Subject: Re: AMBER: mm_pbsa

From: Ray Luo (rluo_at_uci.edu)
Date: Tue Nov 08 2005 - 23:26:52 CST

Did you patch bugfix.48 for pbsa? Are you sure you have used the same
radii for pb and gb?

Wei Chen wrote:

>Hello, all Amber users,
>
>I am using mm_pbsa in Amber8 to calculate binding free energy of two-protein
>binding. When I used PB or GB to calculate polar solvation energy, I got very
>different values. The free energies (not including entropy) are 93.28+/-90.46
>kcal/mol with PB and -37.43+/-5.54 kcal/mol with GB. First of all, the mean
>value with PB is positive, which doesn't make any sense. And the standard
>deviation with PB is so large that it is the same order as the mean value. The
>value with GB seems to be more acceptable. However, I think that GB is an
>approximation to PB. So anybody can help me to understand the results?
>
>Thanks!
>
>Wei Chen
>
>--
>
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-- 
====================================================
Ray Luo, Ph.D.
Department of Molecular Biology and Biochemistry
University of California, Irvine, CA 92697-3900
Office: (949)824-9528         Lab: (949)824-9562
Fax: (949)824-8551          e-mail: rluo_at_uci.edu
Home page: http://rayl0.bio.uci.edu/rayl/
====================================================

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